It's no secret that the current crafting system in STO, is woefully inadequate. Compounded by the fact, that the gear available is generally sub-standard to what is obtainable via STF vendors. What I propose, is to take certain aspects from another MMO, which could function quite nicely within the Star Trek IP.

Essentially, the materials you spend on building something, should also have a chance to be refunded (with some loss), by reverse-engineering it. In the example above, not all of the materials listed would be returned at the same time, but rather a "chance to" obtain them. The cost in materials would most certainly increase as a response to having easier access to the materials. Instead of grinding "Scanning anomalies" all day long, you'd have a chance to gain materials via reverse-engineering.

By being able to reverse-engineer any of the gear that drops in the game, this would also allow easier access to "Phaser" tech for Klingons, or "Disruptor" tech for Federation, since neither side can currently craft (by default) the opponent specific technology.

Crafting "Critical Success":

If you follow a system similar to SWTOR, reverse-engineering the "Mark X Phaser Beam Array" should have a chance of granting you a new recipe, like "Mark X Phaser Beam Array [Dmg]". Reverse-engineering a dozen or so "Mark X Phaser Beam Array"'s could result in multiple variations of the original item. One with superior Damage, increased Accuracy, increased critical hit chance etc.

Additionally, I would tie the "crit chance" of the reverse-engineering process into the "Engineering" commendation category of the Duty Officer system. The chance increases, the higher Tier you achieve, with a set "base chance to critically craft". Crit Chance would also effect the amount of materials returned when reverse-engineering. If a normal reverse-engineered item gives 5-10 Anomalies, a critical item might provide you with 10-15 Anomalies, and a chance to return 1 or more of the more complicated materials (Exotic Anomalies, Common Materials, Uncommon Materials).

Gear Transmutation:

Next step to that, would be to have a form of "transmutation" process, to create items similar to the Spiral-Wave Disruptors. Take 2 items or recipes, and being able to "merge" them into a 3rd new recipe, with aspects of both of the original items. The possibilities would be quite interesting if you'd "transmute" a Tetryon Beam Array, with a Plasma Beam Array (Beam array with a chance to reduce shields AND apply a plasma fire proc). The transmuted variant would have a lower maximum damage potential, but gain the benefit of additional procs. Also, for obvious reasons, you wouldn't be able to transmute a Torpedo Tube, with a Beam Array. Needs to be 2 items of a similar type.

The possibilities become endless with a transmutation system in place. Add to that, the possibility of achieving variations of a recipe, with the various Dmg, Acc, Crit modifiers, and you'll get a whole slew of new items. If you take a Mark X Phaser Beam Array [Dmg] and pair it with another Mark X Phaser Beam Array [Dmg), the damage dealt would be retained, with a small chance of gaining a [Dmgx2] modifier (for a single array).